Ghost in the Machine
by RedCrimson
Summary: An unknow connection to Stella is a result of his past connection to someone else. Now new ememies are after him, Lacus, Cagalli, and others from his past. Reboot of nick2951 original fic, Ghosts.


**A/N: I do not own gundam seed or any factors of the franchise.**

**With permission from nick2951, I have started this reboot to his original fic, Ghosts.**

**I will change a few things, but most things I will keep the same from his original version.**

* * *

As the rain fell, a man dressed in dark slacks and a black trench coat ran through the streets in a desperate hurry to escape the men he was sure were not too far away. His feet splashed through puddles which soaked his pants. But he didn't care right now, his future well being was more important than that state of his attire.

Stopping in a nearby doorstop, he caught his breath and looked behind him to see if the coast was clear. Not seeing anything in view, he breathed a sigh of relief and checked his watch. He only had an hour to arrive at the airport for the flight out of the country with Doctor Chanka.

Navigating through the streets of Hong Kong, he forced himself to ignore the homeless people that scattered about the streets of the run down section of the city. It was too dark to see their faces and the rain did not help. Like many he knew that it was sad to see people living in these conditions, but right now he had to focus on making sure the task that he and Chanka were involved in was taken care off at all cost.

He was unfortuanlty distracted that he never noticed soon enough that he was suddenly grabbed and pulled into a nearby ally by two large men in black, and dragged to the back of the ally until they reached a closed off section in which made escape impossible for him.

Thrown against the wall roughly, the man fell to the ground. As he struggled to pick himself up, he looked at his captors, asian and about in their late twenties. They also were quite muscular and had tattoos all over their arms.

"Hello Doctor Davidson" greeted a voice from the shadows. The man's eyes widened as a tall Caucasian man stepped out of the shadows from behind the two Asians.

"Mr. Nelson" said Davidson with fear in his voice.

"Did you think you and Doctor Chanka could hide from me?" said the man. He was dressed in a gray business suit and had blond hair. He had brown eyes and spoke in an Australian accent.

"What do you want?" asked the Doctor as he leaned against the wall in fear.

"I think you know. Where is it, the last component for my weapon, where is the girl?" answered Nelson with intimidation.

"I don't know" he lied.

"Please don't make me have to force it out of you Doctor, I rather not waste the time" said Nelson in annoyance.

Seeing that he could not persuade his captors, he defiantly yelled "I'll never tell you anything."

"I rather doubt that" said Nelson in amusement. He made a motion with his head and one of the Asians stepped forward.

Reaching into his pocket, the man pulled out a weird looking instrument that Doctor Davidson recognized. Backing away, his eyes widened in horror as the Asian approached.

For the next few minutes, horrible screaming ripped though the city clock. Though it was heard by everyone, not one person investigated or summoned the authorities. When the body was discovered, no one came forward to say what they saw.

A couple of more minutes later, the ally only held the remains of a body left behind. The man known as Nelson left the ally with his two lackys and moved into a van that drove off. He took a phone out of his pocket and after dialing a number, spoke into the reciver.

"Prepare all forces to move out, the target is heading for Orb."

* * *

At an airport a good distance away, Doctor Chanka checked his watch, noting his assistant's lateness. Davidson was never late for anything, so Chanka deduced that the man was not coming, and not in the tardy sense.

"Such a shame, may you rest in peace my friend," he said scilently.

He picked up his suitcase and made his way to the transport bound for Orb. He was glad that he did not divulge the location of the girl to his assistant or their destination. Nelson would stop at nothing to get the girl. Wrapping his brown trench coat closer to himself to fight off the cold, he boarded the transport with the other passengers.

Taking a seat, he turned and smiled at the woman next to him, but she looked away. She was gripping her hands together as a twitching feeling was going through them. Chanka sighed and leaned back to relax in his chair. Once they arrived in Orb, he knew they would be safe. Nelson might have considerable influence, but he was nothing in Orb.

Chanka began to think of ways of getting in contact of Representative Athha directly. It would be quite difficult and he did not foresee much success. But she was involved in this, whether she would want to admit or accept it.

As the transport lifted off, he closed his eyes to take a short nap. A sudden thought came to him and he opened his eyes. Though he could not get to Orb's leader, he knew that there was a chance to go through someone close to her. Remembering a name that came up from his conversations with the girl next to him, he smiled.

The one who was the other half of the key he discovered not too long ago.

Kira Yamato

* * *

**A few days later in Orb…**

22 year old Kira Yamato climbed the small hill, heading towards the grave stone at the top. He was dressed in very casual clothing and carried a bouquet of roses in his hands. When he reached the top, he stood in front of grave and laid the flowers in front of it.

The expression on his face was one of sadness. Out of all the people he had fought to protect, she was the one that he wanted to save the most. However, he failed and she was killed in front of his eyes. The wound of that death still hurt and would probably never close.

"Hi, I know it's been a while and…. I am sorry for that. Things got in the way of me visiting you for a long time now, but it's in the past now.

Funny, I say its in the past, but the past is all I can think of lately.

I have new news; Mu and Murrue have finally set a date for their wedding. It'll be in two months and everyone is planning for it. I'm happy for the both of them and wish I could be as happy as them.

Miriallia's gone back to being a reporter and is doing quite well. Dearka's still chasing after her but she keeps blowing him off.

Sai's actually married now, I hear that he has a kid on the way. I am glad that he was able to avoid the last war and find happiness, a lot of our old friends have," he said, but sighed after that last statement.

"I'm not sure of anything right now in my life, especially my relationship with Lacus.

All we ever do now is fight ever since she returned to lead the PLANTs. She is too afraid to leave her position because she feels that the peace we all worked hard for will collapse in her absence. It seems in our fight to achieve peace; our happiness together had to be sacrificed.

He looked at the grave closely again, and kept talking,

"I miss you Flay; more than ever now. Since breaking up with Lacus, I feel so lonely. All my thoughts have gone back to you lately, my mind keeps wondering about us. Why did you have to leave me alone?

I know…it's a stupid thing to say since you had no control over your death.

I keep thinking, what would have happened if you had survived. Would we have fixed things between us, would I have stayed with you or still gone with Lacus.

If I had stayed with you, would we have progressed to more than what we were?

Would we have married, would we have had a family, would we have been happy?

I don't know why, but it's been eating me at the back of my head lately.

I miss you Flay,

I know it sounds cliché, but I would give anything to see your face again right now.

* * *

"How long do you think he's gonna stand there?" asked Shinn Asuka, leaning against the car with his hands in his pockets.

"As long as he wants, I suppose" answered Athrun, standing next to him as he also eyed his friend from a distance at the grave stone

"Well I hope he hurries up; the party is about to start soon" said Lunamaria with a frown.

"Why are you in such a rush Luna?" asked her sister Meyrin with a smile.

"She's just afraid of ticking off Cagalli" said Athrun.

"Well it is her party, it would be rude to be late" said Luna defensively.

"Well it won't be our fault, Kira was the one who wanted to stop here," said Shinn out of annoyance.

The four of them watched as Kira talked to the gravestone for a good while. They were too far away to hear what the boy was saying. They watched as he laid the roses in front of the tombstone.

"Whose headstone is that anyways?" asked Shinn out of curiosity. When Kira had asked them to make a detour before heading to the Athha mansion, Athrun agreed as turned the car in the direction Kira wanted to go. He had a suspicion where they were going but did not say anything. There was a look in Kira's eyes and Athrun knew that look well.

"A woman whom he knew…and loved from the first war" answered Athrun with a neutral expression.

The trio seemed puzzled at this. "I thought Kira was with Ms. Lacus in the first war?" said Meyrin. After all, that was what she and everyone assumed. They made such a cute couple; it was hard to believe they weren't each other's first loves.

"Kira and Lacus only got together after the war or at its end, I never really got it. Before that, he was with a girl named Flay Allster" answered Athrun.

"I didn't hear anything about that from all my conversations with Ms. Lacus" said Meyrin, surprised. Mrs. Lacus gave off the impression that she was Mr. Yamato's first girlfriend.

"That's because Lacus never wants to talk about her. Flay is rather a sore subject to talk about with her" said raven-haired boy.

"Then how do you know about Flay" asked Shinn.

"From what Cagalli told me; however, she had a lot of unpleasant things to say about her" said Athrun with a shrug.

"Like what?" asked Luna.

"That Flay was a spoiled girl who manipulated Kira and used him. That she messed with his emotions and left a scar that he never healed from" answered Athrun with a frown.

"If that's true, why does he mourn for her?" asked Shinn in disgust for the girl.

"I think because it was a lot more complex than that. There was definitely more to their relationship than Cagalli says. I think more rather Cagalli just exaggerates who Flay was because she was just being the part of the sister hating the girl her brother was dating, and because she feels she has to defend Lacus image in Kira's mind because she her friend and is suppose to hate Flay in response.

Unfortunately, Kira never says anything about their past and I don't ask" answered the boy.

The conversation stops as Kira approaches the car. Arriving, he nodded that he was done and the five of them climbed into the red car with Athrun driving, Kira in the passenger seat, and the rest in the backseat. There was silence in the car with none of the passengers having the courage to ask about the visit.

Neither of them would have noticed someone nearby hiding behind a tree near the grave. After they left, the figure placed a single flower on the grave, and left right after.

* * *

The servant grabbed everyone's jackets as Kira and the gang walked inside the mansion. They knew that they were late but Kira seemed not to care if Cagalli got mad at him for it. Speaking of Cagalli, as they entered the ball room, they spotted said girl talking to a few parliament members and the ambassador from the Atlantic Federation. She was dressed in blues slacks and a white over coat with decorations symbolizing her office. Her hair had also grown out a bit now, the closest she would probably get more feminine appearance.

Noticing the new arrivals, Cagalli excused herself and made her way to them with a scowl on her face. Shinn and Luna took that as a sign to get away and made their way to get something to drink. As Meyrin turned to escape, she stopped and looked at Athrun. Athrun made a motion with his head and Meyrin gave him a quick kiss on the lips before she moved to follow her sister and Shinn, guessing that mount Cagalli was going to blow.

"You were supposed to be here forty-five minutes ago. What took you guys so long?" demanded Cagalli angrily crossing her arms.

"We had to make a stop" answered Kira with an emotionless expression.

"A stop to where?" asked the blond, confused.

Neither Kira nor Athrun said anything to the girl. It took Cagalli a few minutes for it to register and then she finally understood. Deciding to let the matter drop for once, she turned and walked off leaving the two alone.

"That was close; I thought she was going to kill us" said Athrun half jokingly.

"Yeah, I guess" said Kira with a frown and a careless expression.. Both he and his sister had gotten in an argument over the issue of visiting the grave before. It had ended in a yelling match and the two never brought it up again. Cagalli just wouldn't accept that Kira still loved a girl that wronged him.

Lacus had supported him, but in truth he suspected that she was saddened by the prospect of another woman in his heart and hoped he would move past it in time before they had their break up.

Athrun left to join Meyrin, Luna, and Shinn leaving Kira alone to his own devices. Looking around, he saw numerous important Orb Government officials as well as diplomats from other nations.

He felt very lonely. It had been three months since he had last been together with Lacus. There last time together had ended with a huge argument with her decision to stay on as Chairman of the PLANT Council. They had said some hurtful things to each other in front of a few others in her office and Kira had left in anger, saying that he going back to Earth alone as he left the room. He never looked back to see her expression and still wondered what her expression was. Both he and Lacus had not spoken since.

Taking a glass of Champaign and walking to the window overlooking the night-filled horizon, Kira silently toasted to the anniversary of the end of the first war. Though the Second Bloody Valentine War was more eventful, the first always seemed more important to him. He figured it was because of all the people he lost in the various battles. That did not happen in the second war. He actually gained more friends at the end.

He took a sip, and looked at the night sky through the window at the stars. There was a saying that the stars represented loved ones that were no longer in this world. If that were true, he wondered if the star he was thinking about was among them.

He silently stood there and sipped his drink for about ten minutes when a tap on the shoulder caused him to turn around. Cagalli stood there with a sad smile on her face. "Are you alright?" she asked.

"I guess so" answered Kira with a small smile.

"Liar" said Cagalli.

"How do you know that?" asked Kira, raising an eyebrow.

"I am your sister; remember?" said Cagalli smugly.

"I am just feeling a little lonely" said Kira sadly.

Cagalli gave a reassuring smile. "You are not alone here Kira; I am here and so is Athrun as well as all of our friends."

"Yeah, but I wish Fla….Lacus was here" said Kira with a sigh.

"What Lacus is doing is important. We have to maintain this peace or all will fall into chaos once again" said Cagalli, not showing if she was obvious to what he started to say or was ignoring it.

"Even at the cost of individual happiness?" asked Kira bitterly.

"Some sacrifices have to be made" stated Cagalli in a matter of fact tone of voice.

"Maybe I don't want to make that sacrifice. I've given enough to the world, maybe I should get something in return" said Kira with anger rising in his voice and looking down at the floor.

"Now you are sounding like a young kid. Life is harsh Kira, I though you would have learned that by now" said Cagalli angrily.

Kira raised his head up and glared at the girl. Without thinking out his words, he angrily exclaimed "I am sorry that I don't have an unfeeling heart like you Cagalli. I am sorry that unlike you, I choose to try to fight for my love rather than let it go because of my duty. Maybe if you focused a little more on love than duty, you still be with Athrun instead of all alone."

Cagalli's expression went to shock at her brother's words. Her eyes widened and her mouth opened ever so slightly. The people who were the nearest to the siblings were surprised at Kira's outburst and watched what the Orb leader would say.

Realizing that they were making a scene, Kira said, "Sorry, I need some air."

Kira never gave her a chance to respond as he shoved his way past her, almost knocking her to the ground. Exiting the ballroom, he went straight to the closet to grab his coat. While grabbing his coat, he reached into the pocket of Athrun's coat to grab the car keys. Once in hand, Kira turned around and opened the front door and walked outside, slamming the door behind him.

Marching down the steps, Kira walked in the darkness towards the car. He was glad that Athrun had decided to park in front of the mansion instead of where the rest of the guests had parked. It made it easier to escape.

Figuring that he would just go for a quick drive to let off some steam before picking up Athrun and the rest of the gang, he unlocked the driver's side door and climbed inside. Starting up the car, he was about to put into drive when he noticed that the gate was still closed.

Groaning, he opened the door and got out of the car. Walking up to the gate, he pushed against the large metal obstacle and slowly moved it forward. When he was satisfied that it was wide enough to go through, he started to head back towards the car.

As he neared the vehicle, there was a sudden explosion in front of him and he was thrown back against the metal gate. As he fell to the ground, there was a sudden ringing in his ears as well as a great pain to his back and head.

As he lay on the ground, he could barely make out the yells of people around him. Flaming debris was spread around the area, the last thing kira saw was the fire spread to one of the flowerbeds near the gate. His barely opened eyes viewing the flaming roses in front of him as blood started leaking from his head, and then he blacked out.

* * *

In another location, a young woman was holding her head in pain, a sudden pain surging through her whole body as if she was experiencing pain from another source, or possibly another person. Chanka had to sedate her before she went out of control. He had to put her into a stasis pod of some sort in the event that she woke up and still experienced the same panic attack.

Between Nelson's forces searching for him, and the girls panic attacks, he knew he would need to find Yamato and soon. He managed to obtain an e-mail address he used, so he typed up a quick message, and then inserted a flash drive and uploaded a photo that he knew would make sure his message got noticed.

"Now we wait," said Chanka.

* * *

**A/N: Hope that those that read nick2951's original fic like this reboot. **

**Read and Review please.**


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